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Old 06-30-2014, 02:30 PM   #13
Location: Prague, Czech Republic

Join Date: Nov 2010
Posts: 40

OK, so this is likely Titanium sequencing, General Library Preparation protocol or Amplicon/paired-end ..., so read length up to 500nt. The best would be to feed it into newbler:

runAssembly -o (Strain name) -mi 90 -ml 80 -consed -scaffold -cpu 2 (Strain name).sff GAIIxdata.fastq

For non-Roche assemblers you have to go with:

sffinfo -s (Strain name).sff > (Strain name).fasta
sffinfo -q (Strain name).sff > (Strain name).fasta.qual

Last edited by martin2; 06-30-2014 at 02:31 PM. Reason: Typo
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